“I have no evidence at this point from what I’ve seen that classified information was disclosed that in any way would have had a negative impact on our national security,” Obama said at a White House briefing.

Petraeus, a decorated four-star general who received widespread praise for the surge strategy in Iraq, resigned as CIA director on Friday, citing an extramarital affair.

Numerous federal government officials have told NBC News that the married general had a relationship with his biographer, Paula Broadwell, 40, who authored “All In,” a book about Petraeus’ leadership philosophy.

Obama brushed aside questions about whether he felt he should have been notified sooner of the investigation of Petraeus.

“Obviously, there’s an ongoing investigation. I don’t want to comment on the specifics of the investigation, Obama said, “The FBI has its own protocols in terms of how they proceed. … I have a lot of confidence in the FBI.”

The president was not informed of the FBI investigation that revealed Petraeus’ affair until Nov. 8, one day before he accepted his resignation.

FBI investigators who looked into a series of anonymous threatening emails sent to Tampa, Fla., socialite Jill Kelley later determined they were authored by Broadwell, multiple government and law enforcement officials have told NBC News.

Investigators have looked into whether Broadwell violated cyber-harassment laws or improperly possessed classified information, and Obama indicated that the investigation was “ongoing.” Law enforcement officials say they have developed no evidence indicating that Petraeus improperly provided classified information to Broadwell.

Earlier on Wednesday, NBC News confirmed from a veteran senator that Petraeus will testify Thursday about the attack on the U.S. diplomatic mission in Benghazi before the Senate Intelligence Committee.

The Thursday hearing will be the first formal congressional inquiry into the September attack that killed U.S. Ambassador in Libya Chris Stevens, information management officer Sean Smith and security personnel Tyrone Woods and Glen Doherty. Petraeus is also scheduled to appear at a closed hearing of the House Intelligence Committee on Friday.

Republican lawmakers have criticized the administration’s evolving explanation of what triggered the Benghazi attack. Officials early on said it was a spontaneous reaction during a protest about an anti-Islamic film. Later, it was termed a planned terrorist attack.

Commenting on the scandal involving General Petraues, President Obama says he's not aware of any breaches of national security resulting from the scandal.

Questions have also been raised about whether the consulate had adequate security and whether the State Department responded appropriately to requests for more protection.

Military analyst Col. Jack Jacobs (Ret.) said the sex scandal will affect the way Petraeus is questioned by Congress, because members were kept in the dark about the FBI inquiry that led to his resignation.

“It will be interesting to see what tenor it takes and what the senators and congressmen, assuming he gets before both houses, have to say before talking to him. As you know, these hearings have a tendency to be less a question and answer period than it is an opportunity for the members to vent their spleen or talk about what they want to, so that part will be very, very interesting,” Jacobs said.

“In terms of extracting real information about what actually took place and what role the CIA had in what took place in Benghazi, I believe that investigation will determine that they had no role, that by the time the CIA could do anything, it was all over.”

NBC's Michael Brunker contributed to this report.

President Obama says he will "cooperate in any way that Congress wants" in an investigation around the attack on the U.S. consulate in Benghazi while saying his administration did "everything we could to makes sure we protected our people."

NBC's Chuck Todd discusses the political fallout from Petraeus-Allen scandal, noting that the White House national security team is probably more worried about wobbly leadership at the CIA and in Afghanistan than political damage.